The nucleosome is a basic unit to build up the extremely complicating chromatin structure inside the cells of eukaryotes. In the nucleosome, the genomic DNA is wrapped around a histone octamer which is composed of two copies of four different core histone subunits, H2A, H2B, H3 and H4. Mutations in the genomic DNA sequence could cause aberrant expressions of essential proteins that are required to maintain homeostasis of life, leading to serious illness such as birth defects, diabetes, neurological disorders and cancer. However, it has been shown for the past few decades that, even without the sequence alterations, the production and biological functions of the proteins can also be perturbed by newly termed “epigenetic” changes in the genomic DNA and histones. DNA methylation and histone post-translational modifications are two major epigenetic events that are commonly occurred in most of living organisms. In humans, about 70% of cytosines within CpG dinucleotides are usually methylated and the N-terminal tails of the histones are subjected to several covalent modifications including methylation, acetylation, phophorylation, ubiquitination and sumoylation (Shilatifard, A. Annu. Rev. Biochem. (2006) 75, 243-269). At some specific lysine residues of the histones, one, two or three methyl groups can be added or removed by two distinct classes of enzymes, histone methytransferases (HMTs) and histone demethylases (KDMs), respectively. These methylation states play an essential role in regulating gene expression in a context-dependent manner. For instance, di/tri methylation on the lysine 4, 36 or 79 of the histone H3 is generally attributed to an active mark for gene expression. In contrast, di/tri methylation on the lysine 9, 27 of the H3 is usually linked with a closed chromatin conformation (heterochromatin), leading to repression of gene expression (Martin, C. & Zhang, Y Nat. Rev. Mol. Cell Biol. (2005) 6, 838-849).
More than 30 KDMs have been found in mammals and KDMs can be classified into two families based on the underlying mechanism by which they remove methyl groups from the histone tails; LSD1 (lysine specific demethylase 1) and JmjC-containing KDMs. LSD1, the first hisone demethylase discovered in 2004, erases mono- and di-methyl marks on the H3K4 and H3K9 using flavin as a cofactor. As a protonated amine in the substrate is required for its demethylation pathway, LSD1 cannot act on tri-methylated lysines. The existence of different class of KDMs that could remove a trimethyl mark was, therefore, predicted and identified later as catalytic JmjC-domain containing proteins. Compared with LSD1, these proteins contain much more diverse subfamilies including KDM2, KDM3, KDM4, KDM5, KDM6 and PHF2/8, all of which utilize Fe(II) and α-ketoglutarate (αKG) as cofactors (Spannhoff, A. et al. ChemMedChem (2009) 4, 1568-1582)
Many studies have shown that KDMs are implicated in the etiology of cancer, one of the most devastating human diseases (Cloos, P. A. et al. Genes Dev. (2008) 22, 1115-1140). LSD1 is overexpressed in various types of cancer cells including prostate, lung and breast cancer in which LSD1 may enhance oncogenic properties of the cells by modulating the expression of pro-survival genes and tumor suppressor genes such as p53 (Scoumanne, A. & Chen X. J. Biol. Chem. (2007) 282, 15471-15475)
Small hairpin RNA (shRNA)-mediated depletion of KDM2B (also known as FBXL10) attenuated the growth of acute myeloid leukemia (AML) cell line, in which KDM2B is overexpressed (He, J. et al. Blood (2011) 117, 3869-3880). Alterations in the expression of Polycomb target genes may account for this anti-proliferative effect on the basis of a recent finding that KDM2B regulated the expression (Tzatsos, A. et al. J. Clin. Invest. (2013) 123, 727-739).
Initially identified as a putative oncogene GASC1 (gene amplified in squamous cell carcinoma 1), KDM4C, which removes di- and tri-methyl marks from H3K9 as well as H3K36, is genomically amplified in breast carcinoma and prostate carcinoma and required for the growth of these malignant cells (Liu, G. et al. Oncogene (2009) 28, 4491-4500; Wissmann, M. et al. Nature Cell Biol. (2007) 9, 347-353).
The family of KDM5/JARID1 (Jumonji AT-rich interactive domain 1) in human comprises four members, KDM5A/RBP2, KDM5B/PLU-1, KDM5C/SMCX and KDM5D/SMCY, which share highly conserved structural motifs that include a JmjN domain, a catalytic JmjC domain, an ARID DNA binding domain, a zinc finger and two to three PHD (plant homeodomain) fingers. These subfamily members are shown to be involved in the pathogenesis of cancer.
Aberrantly high expression of KDM5A is often found in gastric and cervical cancers (Zeng, J. et al. Gastroenterology (2010), 138, 981-992; Hidalgo, A. et al. BMC Cancer (2005) 5, 77), and KDM5B is also up-regulated in several malignancies such as breast, prostate, lung cancers and melanoma (Lu, P. J. et al. J. Biol. Chem. (1999) 274, 15633-15645; Xiang, Y. et al. Proc. Natl. Acad. Sci. USA (2007) 104, 19226-19231; Hayami, S. et al. Mol. Cancer (2010) 9, 59; zur Hansen, H. Virilogy (2009) 384, 260-265). Acquired drug resistance in cancer is often linked to the presence of cancer stem cells which are capable of reforming tumor cells. Recent studies demonstrated that, in drug-resistant lung cancer cells and melanoma cells, disruption of KDM5A or KDM5B enzymatic function by RNA interference reduced the cancer stem cell-like properties and increased drug sensitivity, thus exerting an anti-proliferative effect on those cells (Sharma, S. et al. Cell (2010) 141, 69-80; Roesch, A. et al. Cancer Cell (2013) 23, 811-825).
KDM5C seems to be associated with mental retardation and some forms of cancer. Gene expression analysis for clear cell renal cell carcinoma (ccRCC) revealed that truncation mutation of KDM5C was found in 3% of ccRCC tumors and most of the mutation was occurred concomitantly with VHL (Von Hippel-Lindau tumor suppressor) mutations (Dalgliesh, G. L. et al. Nature (2010) 463, 360-363).
Although direct linkage between KDM5D and cancer has yet to be known, one study shows that 52% of tested prostate cancer cases contain deletion of KDM5D gene, implying an association of KDM5D with the disease (Perinchery, G. et al. J. Urol. (2000) 163, 1339-1342).
Similar to KDM5A and KDM5B, KDM7B (also known as PHF8) enzymatically active on H3K9me1/2 and H4K20me1 is exhibited to govern an anti-cancer drug (retinoic acid) response in acute promyelocytic leukemia (Arteaga, M. F. et al. Cancer Cell (2013) 23, 376-389).
Taken together, deregulation of KDM is involved in initiation, maintenance, progression and other pathogenesis of cancer, suggesting KDM is a very promising therapeutic target for the intervention of the disease. The present invention is directed to KDM inhibitory compounds with marked potency, thereby having an outstanding potential for a pharmaceutical intervention of cancer and any other diseases related to KDM dysregulation.